Mercurial > repos > lldelisle > incucyte_stack_and_upload_omero
view upload_omero.sh @ 1:3c942429f610 draft default tip
planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit de447190f0743b7f6a3b85e13f712fc07682af3c
author | lldelisle |
---|---|
date | Thu, 21 Dec 2023 17:04:46 +0000 |
parents | e1cba36becb2 |
children |
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#!/bin/bash omero_server="$1" omero_user="$(cat $2 | awk 'NR==2{print $0}')" omero_password="$(cat $2 | awk 'NR==3{print $0}')" to_create=$3 screen_name_or_id=$4 if [ "$to_create" = "create" ]; then # Create a screen: screen_name_or_id=$(omero obj -s ${omero_server} -u ${omero_user} -w ${omero_password} new Screen name="${screen_name_or_id}" | awk -F ":" 'END{print $NF}') echo "Just created the new screen ${screen_name_or_id}" fi echo "Start upload" companion_file=$(ls output/*.companion.ome) omero import -s ${omero_server} -u ${omero_user} -w ${omero_password} -T Screen:id:"${screen_name_or_id}" "${companion_file}" 2>&1 echo "Upload finished"